Hi Michael:
Michael Tiller wrote:
I'm evaluating a couple of different data storage schemes but I'm having
some difficulty with netCDF. First, let me say that I am much happier
with the netCDF Java interface than with the way it is handled in HDF5.
The fact that the netCDF stuff is not just 100% Java but also done the
way a Java interface would normally done has made getting started very easy.
However, I do have some problems. I looked in the User's guide and
tried putting together some example code based on what is found in
Appendix A and I've run into several problems. First let me list my
questions and comments and I'll include my sample code (written as a
JUnit TestCase) at the end:
1. FYI, I'm using netCDF 2.2.12.
2. The example code in the user's guide seems "out of date". Some of
the constructs (use of default constructor for
NetcdfFileWriteable, use of Class object arguments in addVariable)
are now deprecated in the library.
yeah, its way out of date, sorry.
3. Is there a "bug tracker" for netCDF? Just sending stuff to a
mailing list seems like a recipe for falling through the cracks.
not yet, but we're working on one.
4. I get an error when trying to use the NetcdFileWriteable(String
file) constructor (it says "Not a netCDF file" or something like
that). I added the fill argument and now things work?!?
new NetcdFileWriteable(String file) is for opening existing files for writing.
new NetcdFileWriteable(String file, boolean fill) is for creating new files.
In the latest version (2.2.13) these are deprecated in favor of static methods
NetcdFileWriteable.openExisting(..)
NetcdFileWriteable.createNew(..)
5. I'm trying to simple record some time series data. So I created a
dimension for "time" (i.e. a 1D dataset). The idea (in the code
below) is that "h" should be a function of "time". Am I doing
that write? It doesn't seem like anything in that code
distinguishes "time" as the independent variable!?!
what you're doing is correct, as far as it goes, the coordinate variable time(time)
indicates that time is the "independent variable". if you want to go another
step, use a convention such as CF
(http://www.unidata.ucar.edu/software/netcdf/docs/conventions.html) or _Coordinate
(http://www.unidata.ucar.edu/software/netcdf-java/CoordinateAttributes3.html)
6. The ArrayDouble.D1 "helper" class seems like it could do much
more. It has special scalar get and set methods, but what about
having "public double[] get()" and "public void set(double [] v)"
methods!?! It would make it much easier to initialize the data.
good idea, ill think about adding
7. I get messages about not being able to load Nexrad and Grib
service providers. What are those about? Do I need those? If
not, can I shut those warnings off?
no, you dont need; ill turn off those warnings.
8. The example code mentions a class called "ArrayAbstract" which
would appear to be handy but I couldn't find it in the jar file.
now called Array
9. The *main problem* I'm having right now is that I get an error
during "file.create()". I get an "IllegalStateException" with the
message "unknown Dimension == time = 4; // (has coord.var)". Any
ideas?
you need the dimension time to be shared, so change to
Dimension time = file.addDimension("time", 4, true, false, false);
Overall, I'm pretty happy with the design of the system, what can be
expressed and the tie in with NcML (which I assume is still ongoing). I
just wish I could get my sample code to work. :-)
thanks for the feedback
Any help would be very much appreciated. Here is the sample code....
import java.io.IOException;
import junit.framework.TestCase;
import ucar.ma2.ArrayDouble;
import ucar.ma2.DataType;
import ucar.ma2.InvalidRangeException;
import ucar.nc2.Dimension;
import ucar.nc2.NetcdfFileWriteable;
public class TestNetCDF extends TestCase {
public void testCreateData() {
NetcdfFileWriteable file = null;
file = new NetcdfFileWriteable("./example.nc", true);
Dimension time = file.addDimension("time", 4, false, false, false);
Dimension dims[] = {time};
/* Add time */
file.addVariable("time", DataType.DOUBLE, dims);
file.addVariableAttribute("time", "quantity", "time");
file.addVariableAttribute("time", "units", "s");
/* Add a dependent variable */
file.addVariable("h", DataType.DOUBLE, dims);
file.addVariableAttribute("h", "quantity", "Height");
file.addVariableAttribute("h", "units", "m");
try {
file.create();
} catch (IOException e) {
e.printStackTrace(System.err);
fail("IOException on creation");
}
double td[] = {1.0, 2.0, 3.0, 4.0};
double hd[] = {0.0, 0.1, 0.3, 0.9};
ArrayDouble.D1 ta = new ArrayDouble.D1(4);
ArrayDouble.D1 ha = new ArrayDouble.D1(4);
for(int i=0;i<4;i++) {
ta.set(i, td[i]);
ha.set(i, hd[i]);
}
try {
file.write("time", ta);
} catch (IOException e) {
e.printStackTrace(System.err);
fail("IOException thrown while writing time");
} catch (InvalidRangeException e) {
e.printStackTrace(System.err);
fail("InvalidRangeException thrown while writing time");
}
try {
file.write("h", ha);
} catch (IOException e) {
e.printStackTrace(System.err);
fail("IOException thrown while writing h");
} catch (InvalidRangeException e) {
e.printStackTrace(System.err);
fail("InvalidRangeException thrown while writing h");
}
}
}
